5Y87 Rna date Aug 19, 2017
title Structure-Based Insights Into Self-Cleavage By A Four-Way Ju Twister-Sister Ribozyme
authors L.Zheng, R.L.Micura, A.Ren
compound source
Molecule: Rna (5'- R(Papcpcpcpgpcpapapgpgpcpcpgpapcpgpgpc)-3
Chain: A, C
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Metagenome
Organism_taxid: 256318

Molecule: Dnarna (50-Mer)
Chain: B, D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Metagenome
Organism_taxid: 256318
symmetry Space Group: P 21 21 2
R_factor 0.202 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.221 108.963 41.794 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.13 Å
ligand MN enzyme
Primary referenceStructure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme., Zheng L, Mairhofer E, Teplova M, Zhang Y, Ma J, Patel DJ, Micura R, Ren A, Nat Commun. 2017 Oct 30;8(1):1180. doi: 10.1038/s41467-017-01276-y. PMID:29081514
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (5y87.pdb1.gz) 32 Kb
  • Biological Unit Coordinates (5y87.pdb2.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 5Y87
  • CSU: Contacts of Structural Units for 5Y87
  • Structure Factors (762 Kb)
  • Retrieve 5Y87 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y87 from S2C, [Save to disk]
    • View 5Y87 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5Y87
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5y87_D] [5y87_B] [5y87_C] [5y87_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5Y87
  • Community annotation for 5Y87 at PDBWiki (http://pdbwiki.org)

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